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Evolution Basics: From Primate to Human, Part 1

January 2, 2014Tags:Genetics, History of Life

Today's entry was written by
Dennis Venema.
You can read more about what we believe here.

Note: This series of posts is intended as a basic introduction to the science of evolution for non-specialists. You can see the introduction to this series here. In this post we discuss the evolution of the great apes, and our place within that group.

In the last post in this series, we examined the earliest-known primates. This lineage would continue to expand and diversify, ultimately giving rise to a wide range of forms. Included in this diversity is what we now recognize as New World monkeys, Old World monkeys, lesser apes, and our own group, the great apes (hominids). Crown-group hominids include orangutans, gorillas, chimpanzees, bonobos, and humans; their last common ancestral population; and all extinct species descended from that common ancestral population. Present-day great apes are greatly reduced in species diversity compared to the past – in other words, they are relict populations, surviving in isolated, fragmented habitats. Humans are the sole exception to this pattern in terms of population size, but we too are the sole surviving lineage among our closest relatives, as we shall see.

Full genome sequences are now available for most living great ape species, including humans, chimpanzees, gorillas, and orangutans. These sequences have allowed us to determine that the lineages of these four species branched from each other in the following pattern: humans are most closely related to chimpanzees, then to gorillas, and then to orangutans:

A phylogeny of present-day crown-group hominids (great apes). Numbers in yellow ovals at the branch points indicate the percent DNA identity with humans (excluding deletion and insertion mutations). Genome identity values and speciation times are from Locke et al., 2011.

For many years, it was unclear if humans were more closely related to chimpanzees or to gorillas, but full genome sequences allowed us to resolve the issue. One reason for the (now solved) controversy was that the gorilla and chimpanzee lineages branched off our own lineage in relatively quick succession, and did so with quite large population sizes. As you may recall from an earlier post in this series, rapid branching with large populations can lead to an effect known as incomplete lineage sorting, where some of our own genome is more closely related to gorillas than to chimpanzees. Due to this effect, phylogenies for individual genes sometimes produce a ((human, gorilla) chimpanzee) pattern rather than the overall ((human, chimpanzee) gorilla) pattern. As expected, there are even a tiny number of genes in the human genome that are more closely related to the orangutan version of the gene, as I discussed back in 2011 when the orangutan genome was published. Full-genome sequence comparisons between living great apes also fit the expected pattern: orangutans and humans have sequences 97.4% identical; humans and gorillas, 98.4% identical; and humans and chimpanzees, 99.0% identical. (Note, this value does not include insertion/deletion mutations – so-called “indels” – if it did, the human-chimpanzee value would be ~95%, and the other comparisons would follow the same pattern of decreasing identity).

As an aside, the striking amount of genetic identity between humans and other great apes is sometimes puzzling to non-biologists. How is it that species that are so genetically similar be so markedly different? While we will explore this in more detail later in this series, the brief answer is that, for a complex organism, small changes at the DNA level can bring about quite dramatic changes in form and behavior – and these small changes are of the sort that are readily accessible to evolutionary mechanisms that shift allele frequencies in populations over time.

From hominid to hominin

Having surveyed the hominid crown group (orangutans, gorillas, chimpanzees and humans, their last common ancestral population, and all descendant species of that population), we are now prepared to examine our own branch within it – species more closely related to us than to chimpanzees. Such species are known as hominins. Though humans are the only surviving hominin lineage, there was once a wide diversity of hominin species on the planet, some of which lived alongside early humans. One interesting fact about our own lineage is that our “branch” emerges from a rather “bushy” phylogeny. There are many hominin forms in the fossil record, and teasing out their precise relatedness to one another is a challenging exercise (for more detail, see the series by anthropologist James Kidder in “For further reading” below). Forms for which DNA sequence is available are easy to place in a phylogeny, but those known only from fossil remains are more difficult to place. Given our forgoing discussion of stem-group and crown-group species, however, we are now prepared to appreciate these fossil hominins for what they are: stem-group species on our own branch, with some species possibly ancestral to our own, or located very close to the branch points with our lineage:

A phylogeny of crown-group hominids (great apes). Humans, together with extinct species more closely related to humans than to chimpanzees, comprise a subset of hominids known as hominins. Extinct hominin groups such as Kenyanthropus, Paranthropus and Australopithecus are near root of the hominin tree (shaded in gray). Other groups such as Ardipithecus, Orrorin, and Sahelanthropus may be within the hominin tree or stem groups that branch off prior to the last common ancestor of humans and chimpanzees.

The area shaded in gray in the above phylogeny is the area of interest. Some forms in the fossil record can be readily identified as stem hominins (i.e. more closely related to us than chimpanzees) whereas others are more ambiguous: if indeed they branch off our lineage prior to our last common ancestral population with chimpanzees, they are in fact hominids, not stem-group hominins:

Some fossil species that may either be closely-related hominids or stem-group hominins are Sahelanthropus tchadensis, Orrorin tugenensis, and two ardipithecine species (Ardipithecus ramidus and Ardipithecus kadabba). Regardless of their precise placement on the tree, these species are close to the last common ancestral population of humans and chimpanzees, and provide some clues to what that ancestral species looked like, and the order in which we acquired our defining characteristics.

One key distinctive of the hominin lineage is bipedality: walking upright on two legs, rather than on all fours. There is some evidence for bipedal locomotion in Ardipithecus ramidus, Sahelanthropus, and Orrorin, though it is controversial within the field. The evidence is best in Ardipithecus ramidus, which appears to have been a facultative biped (able to walk upright as well as on all fours). Since these species all have small brain volumes (under 400 cubic centimeters), this evidence supports the view that bipedality evolved prior to the expansion in brain volume we observe in later, unambiguous hominins. As such it is probable that our last common ancestor with chimpanzees was an ape with a small brain case and facultative bipedality – traits that would then be shaped substantially in our lineage over time.

In the next post in this series, we’ll continue trace the hominin lineage, and examine the australopithecines and early Homo.

For further reading

Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

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beaglelady - #84026

January 2nd 2014

Excellent as usual, Dennis. This is a fascinating topic. One time I got to meet two of the paleoartists who do the reconstructions that bring these ancient hominins to life.

Jimpithecus - #84028

January 2nd 2014

Thanks for the plug, Dennis. I am putting together the first “origins of modern humans” post, which should be finished soon. I am curious to see how our posts will dovetail.

Ankur Patel - #84276

January 23rd 2014

I have heard non-evolutionary creationists claim that the Chimpanzee and Human genomes are only about 70% similar. They cite a 2010 study from Nature called “Chimpanzee and human Y chromosomes are remarkably divergent in structure gene content”. Could someone tell me if this new finding has any weight behind it? And if so, does it challenge our common ancestry with chimpanzee’s and other primates? I’m just a layman who accepts evolution and human ancestry but I haven’t seen any responses to this new finding.